Open Access Highly Accessed Methodology article

Discovering semantic features in the literature: a foundation for building functional associations

Monica Chagoyen1*, Pedro Carmona-Saez1, Hagit Shatkay2, Jose M Carazo1 and Alberto Pascual-Montano3

Author Affiliations

1 Biocomputing Unit, Centro Nacional de Biotecnologia – CSIC, Madrid, Spain

2 School of Computing, Queen's University, Kingston, Ontario, Canada

3 Dpto. Arquitectura de Computadores, Universidad Complutense de Madrid, Madrid, Spain

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BMC Bioinformatics 2006, 7:41  doi:10.1186/1471-2105-7-41

Published: 26 January 2006

Additional files

Additional File 1:

Cophenetic correlation coefficient. This file contains three graphs showing the cophenetic correlation coefficient for the SGD8, Reelin and random datasets.

Format: PDF Size: 577KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional File 2:

Clustering results. This file contains two spreadsheets with the results of the clustering performed on the semantic profiles (also included after z-score normalization) obtained for the SGD8 and Reelin datasets.

Format: XLS Size: 1.1MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional File 4:

Reelin dataset analysis by SVD and NMF. Descriptive comparison of the results obtained by clustering of gene profiles obtained by SVD and NMF algorithms. Includes hierarchical trees.

Format: PDF Size: 24KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional File 3:

Example representation of literature profiles. This file contains the representation of a literature profile for gene PET54 as obtained in the vector space model, a clustered space and the semantic space.

Format: PDF Size: 31KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data